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Development of molecular simulation model for heterogeneous RNA and RNA-protein structures.

   School of Pharmacy

About the Project

In recent years, it has become clear that RNA molecules play active roles in a variety of cell regulatory processes. In addition, RNA molecules have a great potential for therapeutic applications, as evidenced by the success of COVID-19 mRNA vaccines. However, despite advances in molecular biology and bioinformatics, little is known about the molecular structures of RNA in cells and under formulation conditions, especially for long messenger RNA and non-coding RNAs. Molecular simulations are useful for understanding the structure and dynamics of RNA, are an excellent complement to experiments which often provide only indirect information about structures. We develop and apply coarse-grained models to elucidate folding and assembly mechanisms of various RNAs (see references). This PhD project aims to extend the applicability of the models to longer single-stranded RNA and RNA-protein complex structures. Several challenges need to be addressed; some examples are, 1) an efficient sampling algorithm should be developed to simulate diverse structures of long RNAs, 2) design and implement a model of RNA-protein interactions for simulating ribonucleoprotein complexes, 3) simulating RNA structures under complex formulation conditions such as cationic lipids and polymers. The successful candidate will tackle one or more of these biophysical problems with expert academics in computational chemistry and biophysics. Our goal is to understand RNA structures, dynamics, and mechanisms linked to various cellular functions, diseases, and nucleic-acids therapeutics.


o  Due to funding restrictions, the studentship is only available for UK candidates.

o  Candidates must possess or expect to obtain a master’s degree in physics, chemistry, or related science discipline. Equivalent research experience, such as research assistantship, will also be considered.

o  The project is particularly suitable for candidates with a physics or chemistry background who would like to continue or start developing their expertise in computational biophysics.

o  Experience in some form of programming is desired. The project involves writing scientific programs in Fortran and Python.


o Theory and simulations for RNA folding in mixtures of monovalent and divalent cations, Nguyen HT ; Hori N ; Thirumalai D, Proc. Natl. Acad. Sci. U.S.A. (2019) https://doi.org/10.1073/pnas.1911632116
o Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA, Hori N ; Denesyuk NA ; Thirumalai D, Proc. Natl. Acad. Sci. U.S.A. (2021) https://doi.org/10.1073/pnas.2020837118
o Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics, Nguyen HT ; Hori N ; Thirumalai D, Nat. Chem. (2022) https://doi.org/10.1038/s41557-022-00934-z

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